New York (CNN) -- A federal judge Thursday sentenced a Pakistani scientist convicted of attempting to kill Americans in Afghanistan to 86 years in prison.
A jury in Manhattan convicted Aafia Siddiqui on seven charges, including attempted murder and armed assault on U.S. officers, in February. She will serve her sentence at a facility in Texas where she was previously held while awaiting trial.
Prosecutors said Siddiqui picked up a rifle and shot at two FBI special agents, a U.S. Army warrant officer, an Army captain and military interpreters while she was being held unrestrained at an Afghan facility on July 18, 2008. The agents returned fire shooting her in the abdomen.
Afghan police had arrested her outside the Ghazni governor's compound in central Afghanistan after finding her with bomb-making instructions, excerpts from the "Anarchist's Arsenal," papers with descriptions of U.S. landmarks, and substances sealed in bottles and glass jars, according to the charges.
The indictment said Siddiqui had "handwritten notes that referred to a 'mass casualty attack'" listing several locations in the United States and "construction of 'dirty bombs.'" Upon her conviction, the American-educated neuroscientist, blasted the decision as "a verdict from Israel, not America." Siddiqui's family said she had been unjustly convicted.
At her sentencing Thursday morning, the 38 year-old MIT graduate shook her head in defiance and wagged her finger in a "no" gesture as U.S. District Judge Richard M. Berman laid out the case against her.
But Siddiqui was more subdued when Berman allowed her to speak before the packed courtroom filled with family, spectators and foreign and national press.
Clad in a khaki suit and a hijab that covered most of her face, Siddiqui repeatedly asked her Muslim supporters to not "get emotional."
"I don't want any violence in my name," Siddiqui said of demonstrations in her native Pakistan, where her case has become a cause celebre. "If you do anything for me, please educate people about Islam because people don't understand that it is a religion of mercy."
Before the judge sentenced Siddiqui to more than eight decades in prison, defense attorney Dawn Cardi told the court that it was the most difficult case of her career.
"Dr. Siddiqui is an enigma," Cardi said of her client, who had attempted multiple times to fire her team of attorneys hired by the government of Pakistan. Cardi said there were many unanswered questions in her client's case, including where she was between the years of 2003 and 2008, when Siddiqui claims to have been held in a secret prison.
"The government has not admitted to secret prisons or torture. But the information is going to come out," Cardi said, noting that solitary confinement had taken a visible toll on Siddiqui who "had diminished mental capacity."
Since 2003, the whereabouts of Siddiqui had been the source of much speculation. According to Amnesty International, Siddiqui and her three small children were reported apprehended in Karachi, Pakistan, in March 2003, shortly after the FBI issued an alert requesting information about her location.
Several reports indicated that Siddiqui was in U.S. custody after her arrest in Karachi. But in May 2004, then-Attorney General John Ashcroft and FBI Director Robert Mueller identified Siddiqui as being among several sought-after al Qaeda members.
Siddiqui was extradited to the United States in August 2008, after the shooting incident.
"We are going to look back on this era in our country and we are going to say that fear is what drove our sentences," Cardi said.
"Despite the fact that this is a woman of peace who has repeatedly said she doesn't support any acts of vengeance in her name, I fear that the injustice done to her will cause outrage throughout the Muslim world," said Tina Foster, executive director or International Justice Network and spokesperson for the Siddiqui family.
Manhattan U.S. Attorney Preet Bharara hailed the sentence, commending federal and military investigators in the case.
"As a unanimous jury found beyond a reasonable doubt, Aafia Siddiqui attempted to murder Americans serving in Afghanistan, as well as their Afghan colleagues. She now faces the stiff consequences of her violent actions."
But Elaine Sharp, one of Siddiqui's defense attorneys, said, "We just put someone in prison for the rest of her life who is mentally ill."
CNN's Kiran Khalid contributed to this report.